[R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop

Thu Nov 5 23:19:28 CET 2020

Dear Pablo,

Sometimes when building a vignette the lines reported are a bit off (I
usually check the code above and below those lines).
I could reproduce the error on R 4.0.1, the error is triggered on
lines 515-519 on the following code:

relationship_plot(qtl_file=out.qtls.filtered, x="Abbrev", y="Ref_ID",
cex=1,gap=2.5,degree = 60,
canvas.xlim = c(-5, 5),
canvas.ylim = c(-3, 3),
grid.col = color.grid)

Hope you can solve it.

Cheers,

Lluís

On Thu, 5 Nov 2020 at 22:00, Pablo Fonseca <pfonseca using uoguelph.ca> wrote:
>
> Dear Lluís Revilla,
>
> Thank you very much for the comments and suggestions. I changed the vignette format from the BiocStyle to a regular html. However, I am still getting an error.  Now, the error is "Input vector too short" and it is related with the same code chunk lines 465-506.
>
> I can't figure out a possible reason for this issue. Any comment or suggestion will be very welcome.
>
> Kind regards.
>
>
> Pablo Augusto de Souza Fonseca, Ph.D.
> Postdoctoral Fellow at University of Guelph
> Centre for Genetic Improvement of Livestock
> E pfonseca using uoguelph.ca
> W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca
> ________________________________
> From: Lluís Revilla <lluis.revilla using gmail.com>
> Sent: Thursday, November 5, 2020 11:38 AM
> To: Pablo Fonseca <pfonseca using uoguelph.ca>
> Cc: Duncan Murdoch <murdoch.duncan using gmail.com>; r-package-devel using r-project.org <r-package-devel using r-project.org>
> Subject: Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop
>
> CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to IThelp using uoguelph.ca
>
>
> Hi Pablo,
>
> "The magick package is required to crop"  is related to using
> BiocStyle for your vignette. Not sure what causes it, but I reported
> this error some time ago:
> https://github.com/Bioconductor/BiocStyle/issues/77.
> On related issues and on bioc-devel mailing list
> (https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016656.html) it
> is mentioned to use knitr::opts_chunk$set(crop = NULL) to solve it.
> If the package is intended for CRAN I would recommend not using
> BiocStyle template, which would also solve this.
>
> Best,
>
> Lluís
>
> On Thu, 5 Nov 2020 at 17:28, Pablo Fonseca <pfonseca using uoguelph.ca> wrote:
> >
> > Dear Duncan Murdoch,
> >
> > Thank you for the quickly reply. Yes, the package is on Github. Any comment or suggestion will be very welcome.
> >
> > https://github.com/pablobio/GALLO
> >
> > Kind regards.
> >
> > Pablo Augusto de Souza Fonseca, Ph.D.
> > Postdoctoral Fellow at University of Guelph
> > Centre for Genetic Improvement of Livestock
> > E pfonseca using uoguelph.ca  <mailto:pfonseca using uoguelph.ca>
> > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>
> > ________________________________
> > From: Duncan Murdoch <murdoch.duncan using gmail.com>
> > Sent: Thursday, November 5, 2020 11:22 AM
> > To: Pablo Fonseca <pfonseca using uoguelph.ca>; r-package-devel using r-project.org <r-package-devel using r-project.org>
> > Subject: Re: [R-pkg-devel] Error during automatic check for vignette re-building - The magick package is required to crop
> >
> > CAUTION: This email originated from outside of the University of Guelph. Do not click links or open attachments unless you recognize the sender and know the content is safe. If in doubt, forward suspicious emails to IThelp using uoguelph.ca
> >
> >
> > On 05/11/2020 10:55 a.m., Pablo Fonseca wrote:
> > > Dear all,
> > >
> > > Currently I am trying to update my package (GALLO) with some small edits in the code. However, the package is not passing in the automatic check. I am getting only two warnings:
> > >
> > > The first one is a warning related with the maintainer email (my email in the case), which is correct. I really think that this is not the cause of the package failure during the automatic checking.
> >
> > The first one is actually about your version number:  you called it
> > version 1.0, but CRAN already has 1.0.  You need to increase the number.
> >
> >
> > >
> > > The second warning is a problem during the vignette rebuilding. The warning is "The magick package is required to crop". In my first submission I didn't experience this error. In the recent submissions for updates, I included the magick package as a dependency of the package. However, this didn't fixed the issue. Additionally, I can't reproduce the errors in my machines, even when running R CMD check --as-cran. The error seems to be related with the lines 465-495 from the vignette. I double checked the code and introduced some small changes (such as reducing the figure dimensions).
> >
> > I am not sure about this one; I'd need to look at the package to check.
> > Is it on Github?
> >
> > Duncan Murdoch
> >
> > >
> > > Have ever someone faced a similar issue? However, it seems ineffective. Is there any possibility to be a false negative?
> > >
> > > I am sending bellow the links for the check logs.
> > >
> > > package GALLO_1.0.tar.gz does not pass the incoming checks automatically, please see the following pre-tests:
> > > Windows: <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_20201105_154946/Windows/00check.log>
> > > Status: 2 WARNINGs
> > > Debian: <https://win-builder.r-project.org/incoming_pretest/GALLO_1.0_20201105_154946/Debian/00check.log>
> > > Status: 2 WARNINGs
> > >
> > > Last released version's CRAN status: ERROR: 1, WARN: 11
> > > See: <https://CRAN.R-project.org/web/checks/check_results_GALLO.html>
> > >
> > >
> > > Kind regards.
> > >
> > >
> > > Pablo Augusto de Souza Fonseca, Ph.D.
> > > Postdoctoral Fellow at University of Guelph
> > > Centre for Genetic Improvement of Livestock
> > > E pfonseca using uoguelph.ca  <mailto:pfonseca using uoguelph.ca>
> > > W http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca  <http://animalbiosciences.uoguelph.ca/abscpeople/pfonseca>
> > >
> > >        [[alternative HTML version deleted]]
> > >
> > > ______________________________________________
> > > R-package-devel using r-project.org mailing list
> > > https://stat.ethz.ch/mailman/listinfo/r-package-devel
> > >
> >
> >
> >         [[alternative HTML version deleted]]
> >
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